MMSYN1 0611 dpantuso

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Author Information

Danny Pantuso

Basic Information

  • ID: MMSYN1_0611
  • Name: polA
  • Organism: JCVI-Syn3.0
  • Description: DNA polymerase 1 (Pol 1) is a key enzyme involved in the maintenance and replication of DNA. Like most DNA polymerase, it is a vital protein for copying DNA without mutation. Unlike most polymerases, it is unique in that it combines two types of polymerase activities. Pol 1 is responsible for both a 5’ to 3’ exonuclease activity and a 3’ to 5’ proofreading exonuclease activity.

DNA polymerase is especially important to our field in that it was the first known DNA polymerase known of any kind, and is ubiquitous in prokaryotes (Ecocyc.org, 2017). Discovered in 1956, this tiny gene represents a monumental leap in our understanding of bioengineering and has paved the way for countless other cells and mythizations to occur. As a result of their finding this gene, both lead scientists, Professor Arthur Kornberg and Severo Ochoa, earned a Nobel Prize. (Wikipedia, 2017) DNA Pol I is 1 of 5 known DNA polymerases found within E. coli. While they are all vital to the function of the cell, DNA Pol 1 is the most common and thought to be the most important for DNA repair. In an experiment aimed at determining the exact function of DNA Pol I, scientists found that colonies that lacked this gene could grow and reproduce normally. However, when exposed to harmful, mutagen inducing elements such as UV light, the cells became damage and were extremely prone to degradation. In addition, while DNA replication happens at roughly 1000 nucleotides a second, Pol I processes DNA at only ~20 nucleotides a second, and falls off after incorporating only ~50 nucleotides. Thus, scientists concluded that its primary role is repair. DNA Pol I’s is composed of four domains with two separate enzymatic activities. The last domain on the protein proofreads the product of Pol I and can repair any missed base pairs almost immediately after the mistake has been identified. The other three domains function as helper polypeptides to facilitate the DNA polymerase activity.


  • DNA Length: 2787 basepairs.
  • DNA sequence:

ATG AAG ACG AAA ATT CTG GTA GTC GAT GGT AAT TCA CTG ATT TTT CGC GCT TTC TAC GCA ACC GCC TAT TCG CCC AAT ACT AGC TTA CTT AAA ACT AAG AGC GGT GTA TTA ACC AAC GCC GTG TAC TCA TTC ATT AAT ATG TTA CTT AGC GTC ATT CAC CAG CGC GGG CCT TAT GAT CAT ATT CTT ATT GCA TTT GAC AAG GGG AAG AAA ACA TTC CGT CAT GAC CTG CTT TCA GAC TAT AAG GCC AAC CGC ATT AAA ACA CCG AAC GAA TTA GTT GAG CAG TTT TCA GTC GTA CGT GAA TTT CTG ACG AAG GCG AAT ATC CAA TGG TTC GAA CAA GAA AAC ATT GAG GCA GAC GAT ATT GTA GGA TCC ATC TGT AAG TAC GCC GAA AAA CAG TTC GAC AAT CTT CAA GCT GAA ATT TTA TCA TCA GAT AAA GAT ATG TAT CAA CTG ATT ACT AAT AAG GTC ATT TGT CTG AAT CCG GTC CAG GGT GTC AAT GAA CTG GAA GAA GTG GAT ACA AAC AAG TTG TTC GAA AAA TGG CAG ATT TTA CCG AAC CAA GTC CCA GAT TAC AAA GCC ATC GTG GGC GAC AGC TCC GAC AAT CTT AAA GGT GTC AAC GGA ATT GGC CAG AAA GGG GCT ATT AAG TTG ATC CAG CAG TAT CAA AAC CTT GAG AAC ATT TAC AAT AAT TTA GAG CAA ATC AAG GGG GCT ATC AAG ACT AAG TTG GAG CAG GAT AAA AAG ATG GCG TTC TTA TGC AAA GAC CTT GCG ACG ATC AAA ACC GAT GTC ATC TTA GAG AAC TTT TCG TTT AAA AAG TTG GAT TTC AAC GTC GAT AAT ATC TAC GAA TTC TTG AAC AAG TAT GAA ATG TAC TCA TTA AAA AAG CGT TTT ACC AAT ATT TTA AAT TTG GAC TTC AAT CCT TAC CAG AAT AAG AAA CAG AAC CTG GAC GTC AAA ATC ATC AAT TCC TGG TCC AAA GAT TAT GAG GAT TCA ATT AAC TAC CTT TAT GTA GAA AGT CTG GAG GAG GAC TAC CAC AAA GAC AAA ATT ATC GGG ATT GGA ATT TCG AAC AAC AAG GGA AAC TTC TAC TTG GAT TTC AAG AAC AAG GCG CAA CAG TTA TCG TTT TTC GAG GAC ACC ACG CTT AGT TCT ACA GAC TCG TTA TTC GAA GAA TTC CTT AAT AAC AGC AAC TTA AAA AAA TAT ACA TAC GAT ATT AAA AAA ACT ACA TAT CTG TTA AAG AAC CAC AAG TAC AAC GTA CTT GCG TCA AAT TTT GAT TTC GAC TTC ATG GTG GCG TGT TAC TCA CTT AAC GCG AAC GTA GTC TCA GAC TTG TCA AAT CAA ATT AAG TTA GTC GAT AAC TTG ATT GAA TTG GAA ACT ATC GAT CAG ATC TTC GGG AAA GGT GTC AAA AAG AAC CCC GAT ATT GAT TTG GAC ATC AAG AGC AAA TAC ATT TCG AAA AAG GCG TAT TTG CTG AAA AAA TAT AGT GAT CAG TTG ATT GAG CAG TTG AAA CAA ACC AAC ACT TAC GAC TTA TAC TTG AAG ATT GAC CAC CCA CTT ATT GAA GTA CTT TAT GAC ATC GAA GTC CAA GGG ATC TTG ATC GAT AAA GAA CAA CTT AAG TTA CAA ACA CAA CAG ATC CTG AAA AAA ATC AAT CAT ATC GAG GGC CAG ATG AAA ATT TTG GTG GCA GAG GAG ATT GAC AAT AAT TTT AAT TTT AGC AGT CCC AAG CAA ATT CAG GAG TTG CTT TTT GAC AAG CTG AAG CTG CCG AAT CTG GAA AAG GGT ACG ACT AGT AAA GAG GTA TTG GAG AAA CTG ATC ACA TAT CAT CCC ATC ATC AAT TTG CTT TTG GAG CAC CGT AAA TAC ACG AAG TTG TAC ACG ACG TAT CTT AAA GGC TTC GAA AAA TTT ATC TTC GAT GAT TCG AAG GTC CAT ACG ATT TTT AAC CAC ACC TTG ACT AAC ACA GGC CGT TTA TCC AGC TCA TAC CCT AAT ATC CAG AAT ATT TCG ATC CGC GAC AAC GAA CAG AAG GAA GTT CGC AAA ATC TTC ATT ACT AAC AAC AAC AAA ACC TTT TTA TCC TAT GAT TAT AGT CAA ATT GAG CTT CGT GTG CTT GCA CAG ATG AGT AAA GAG ACG AAT TTG ATT AAC GCA TTC AAT CAA AAT GCA GAT ATT CAT CTG CAG GCC GCA AAG CTG ATC TTC AAC TTG AGC GAC GAC CAA ATT ACC TCT GAA CAA CGC CGT ATT GCT AAA GTC TTC AAT TTC GGG ATC CTG TAC GGC CTT ACA GAT TTT GGA CTG GCC TCA GAC TTG AAC ATT TCC GTA AAT CAG GCA AAG CAG ATG ATT AAA GAC TAT TAC AGC GCA TTC CCA TCT TTA TTA GAA TTT AAG GAA AAA CAG GTG GAA ATC GCT ACA TCC CAA GGC TAC ATT ACA ACA TTA TCC AAC CGT CGT CGC TAT ATC AAC GAG TTG AAT TCT ACC AAC CAC AAT ATT CGC CAA TTT GGA AAG CGT ATC GCC GTC AAT ACT CCA ATT CAG GGA ACA GCC AGT GAT ATC TTA AAA GTA GCG ATG ATC TCC ATC TAT AAG AAG CTT AAA GAA CAA AAC TTG GAC GCC CGC ATC GTC TGT CAG ATT CAT GAT GAA ATT ATC TTG GAG GTT GAT GAT AAT CAA CTG GAG CAG ACA AAG CGC ATC GTA GTC TCA GAG TTG GAA AAC GCA CTG GAG AAG CTT TTT TTA GAC TTA AAC ATC AAG GAA CAG GTG GTT GTA AAA CTG AAG GTC GGC GAA TCA GTG GGC AAA ACT TGG TTC GAC TTG AAG taa

  • Amino Acid length: 924 amino acids.
  • Amino Acid sequence:

MKTKILVVDGNSLIFRAFYATAYSPNTSLLKTKSGVLTNAVYSFINMLLSVIHQRGPYDHILIAFDKGKK TFRHDLLSDYKANRIKTPNELVEQFSVVREFLTKANIQWFEQENIEADDIVGSICKYAEKQFDNLQAEIL SSDKDMYQLITNKVICLNPVQGVNELEEVDTNKLFEKWQILPNQVPDYKAIVGDSSDNLKGVNGIGQKGA IKLIQQYQNLENIYNNLEQIKGAIKTKLEQDKKMAFLCKDLATIKTDVILENFSFKKLDFNVDNIYEFLN KYEMYSLKKRFTNILNLDFNPYQNKKQNLDVKIINSWSKDYEDSINYLYVESLEEDYHKDKIIGIGISNN KGNFYLDFKNKAQQLSFFEDTTLSSTDSLFEEFLNNSNLKKYTYDIKKTTYLLKNHKYNVLASNFDFDFM VACYSLNANVVSDLSNQIKLVDNLIELETIDQIFGKGVKKNPDIDLDIKSKYISKKAYLLKKYSDQLIEQ LKQTNTYDLYLKIDHPLIEVLYDIEVQGILIDKEQLKLQTQQILKKINHIEGQMKILVAEEIDNNFNFSS PKQIQELLFDKLKLPNLEKGTTSKEVLEKLITYHPIINLLLEHRKYTKLYTTYLKGFEKFIFDDSKVHTI FNHTLTNTGRLSSSYPNIQNISIRDNEQKEVRKIFITNNNKTFLSYDYSQIELRVLAQMSKETNLINAFN QNADIHLQAAKLIFNLSDDQITSEQRRIAKVFNFGILYGLTDFGLASDLNISVNQAKQMIKDYYSAFPSL LEFKEKQVEIATSQGYITTLSNRRRYINELNSTNHNIRQFGKRIAVNTPIQGTASDILKVAMISIYKKLK EQNLDARIVCQIHDEIILEVDDNQLEQTKRIVVSELENALEKLFLDLNIKEQVVVKLKVGESVGKTWFDL K

Function and Homologs

  • Functional Category: [DNA repair]
  • Product: DNA polymerase I
  • Module: DNA polymerase I
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • DNA polymerase I [Mycoplasma mycoides], 1831 / 100% / 0.0 / 100%, [1]
    • DNA polymerase I [Mycoplasma mycoides], 1811 / 100% / 0.0 / 98%, [2]
    • DNA polymerase I [Mycoplasma capricolum], 1810, 100%, 0.0 / 98%, [3]


  • [EG10746]

Expression

  • Expression Level: Medium.
  • Expression Level Hypothesis: DNA Polymerase I is mainly responsible for the maintenance of DNA, a vital part of cell functioning. Thus, DNA polymerase has a medium expression rate so that the DNA is maintained and cared for, but isn't highly expressed because DNA is a relatively stable molecule and will not break down often. Thus, it is not necessary to have high levels of DNA Polymerase 1.
  • Expression Level References and Description: Mgenitalium database
  • Expression Time: At which time should the gene be expressed in the lifecycle

of our organism? Late

  • Expression Level Hypothesis: The cell does not need to immediately correct for small errors in the DNA.Small scale DNA degradation is often the result of time and decay, so it follows that this protein should be expressed later on the the cell lifecycle.
  • Expression Time References and Description: Gene description.

Gene Context

  • Other Components: dnaN [4]
  • Possible Dependencies: DNA metabolism
  • Process: 3'-5' exonuclease activity
    • Inputs: Deoxynucleoside triphosphate + DNA(n)
    • Outputs: diphosphate + DNA(n+1)

Construct

  • Synthesis Score: The synthesis score of your construct: 1, 2,3
  • Predicted Translation Rate: Prediction of construct translation rate from the RBS calculator
  • Design Notes and Details: For example, had to use a rare codon to fix folding energy;
  • GenBank File: A link to the GenBank file. file